Hi @jramend,
Myself and @jdtournier are both Arch Linux users 
, and I’d hazard a guess that any other Linux machines used by developers are probably Ubuntu. Personally I’m using xfce as my WM, kernel 4.4.48-1-lts on a single GTS 250 (LTS kernel required to keep the older 340.xx video drivers working).
Are you attempting to use bumblebee or similar to deal with the multiple GPUs? I believe @Dave has some experience with that.
It might be worth copy&pasting your configure script log (make sure you format it so it doesn’t clog everybody’s screens!) just in case it contains any hints.
That, or skipping Linux altogether and perhaps choosing to run MRtrix through a Linux subsystem on Windows.
That works for console commands; but as far as I know, nobody has managed to get mrview working through WSL. The Windows installation instructions therefore remain using MSYS2. I use this on my laptop; I still have an annoying recurring issue where the icons in mrview don’t appear, but it works, and the NVidia drivers can be set up to utilise the dedicated graphics card whenever mrview is executed. Unfortunately it does mean that MRtrix3 scripts that depend on FSL commands cannot be used natively.